The cells that constitute different tissues in an organism, although having the same genomic DNA, differ significantly from one another with respect to the specific genes that are expressed and the levels of expression. Differences in gene expression can also be observed when comparing cells that are obtained from a healthy organism and corresponding cells from an organism manifesting a disease state. Other examples of variations in gene expression include changes induced by exposing a cell to a pharmaceutical compound, a toxin, or some other environmental variable. It is of interest to provide methods for analyzing changes in gene expression. Methods of analyzing gene expression find wide use in both research and diagnostics. Additionally, variations exist at the genomic level between cells from different members of the same species, i.e., polymorphisms. Genetic polymorphism may give rise to gene expression difference between species members. Furthermore, polymorphisms may also give rise to phenotypic differences irrespective of the effect of the polymorphisms on transcription. Thus it is also of interest to provide techniques for analyzing nucleotide sequences, including the detection and monitoring of polymorphisms. Moreover, in many instances, it may be of interest to obtain both gene expression data and sequence information in the same experimental procedure. Various embodiments of the invention provide convenient techniques for addressing one or more of these needs for genetic analysis.